A modified nudged elastic band algorithm with adaptive spring lengths.

We present a modified version of the nudged elastic band (NEB) algorithm to find minimum energy paths connecting two known configurations. We show that replacing the harmonic band-energy term with a discretized version of the Onsager-Machlup action leads to a NEB algorithm with adaptive spring lengths that automatically increase the resolution of the minimum energy path around the saddle point of the potential energy surface. The method has the same computational cost per optimization step of the standard NEB algorithm and does not introduce additional parameters. We present applications to the isomerization of alanine dipeptide, the elimination of hydrogen from ethane, and the healing of a 5-77-5 defect in graphene.

Impacted post-traumatic maxillary central incisor: A multidisciplinary approach.

AIM: The aim of this paper is to provide clinicians useful information for the management of impacted central incisor due to early childhood trauma. CASE REPORT: It is reported the case of an impacted right maxillary central incisor in an 8-year-old male patient who had an intrusive luxation trauma of primary tooth at the age of 4. After clinical and radiographic evaluation, a multidisciplinary treatment plan was planned. Therapy involved a surgical and orthodontic approach in order to expose the tooth and move the incisor in the normal position with a self-ligating appliance system. RESULTS: Through a multidisciplinary approach it was possible to move the impacted incisor in the occlusal plane, preserving periodontal tissues and tooth vitality. CONCLUSION: When a permanent tooth is impacted, the multidisciplinary approach of surgery and orthodontic treatment is the best way to obtain a suitable outcome in terms of gingival contour, occlusal plane and aesthetics, when compared with other treatment options.

Quantum Symmetry from Enhanced Sampling Methods.

We address the problem of the minus sign sampling for two-electron systems using the path integral approach. We show that this problem can be reexpressed as one of computing free energy differences and sampling the tails of statistical distributions. Using metadynamics, a realistic problem like that of two electrons confined in a quantum dot can be solved. We believe that this is a strategy that can possibly be extended to more complex systems.

Molecular dynamics simulations of solutions at constant chemical potential.

Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CµMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CµMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

Density functional simulations of Sb-rich GeSbTe phase change alloys.

We generated models of the amorphous phase of Sb-rich GeSbTe phase change alloys by quenching from the melt within density functional molecular dynamics. We considered the two compositions Ge(1)Sb(1)Te(1) and Ge(2)Sb(4)Te(5). Comparison with previous results on the most studied Ge(2)Sb(2)Te(5) allowed us to draw some conclusions on the dependence of the structural properties of the amorphous phase on the alloy composition. Vibrational and electronic properties were also scrutinized. Phonons at high frequencies above 200 cm(-1) are localized in tetrahedra around Ge atoms in Sb-rich compounds as well as in Ge(2)Sb(2)Te(5). All compounds are semiconducting in the amorphous phase, with a band gap in the range 0.7-1.0 eV.

First-principles study of nitrogen doping in cubic and amorphous Ge2Sb2Te5.

We investigated the structural, electronic and vibrational properties of amorphous and cubic Ge(2)Sb(2)Te(5) doped with N at 4.2 at.% by means of large scale ab initio simulations. Nitrogen can be incorporated in molecular form in both the crystalline and amorphous phases at a moderate energy cost. In contrast, insertion of N in the atomic form is very energetically costly in the crystalline phase, though it is still possible in the amorphous phase. These results support the suggestion that N segregates at the grain boundaries during the crystallization of the amorphous phase, resulting in a reduction in size of the crystalline grains and an increased crystallization temperature.

Enhanced sampling in the well-tempered ensemble.

We introduce the well-tempered ensemble (WTE) which is the biased ensemble sampled by well-tempered metadynamics when the energy is used as collective variable. WTE can be designed so as to have approximately the same average energy as the canonical ensemble but much larger fluctuations. These two properties lead to an extremely fast exploration of phase space. An even greater efficiency is obtained when WTE is combined with parallel tempering. Unbiased Boltzmann averages are computed on the fly by a recently developed reweighting method [M. Bonomi, J. Comput. Chem. 30, 1615 (2009)]. We apply WTE and its parallel tempering variant to the 2d Ising model and to a Go model of HIV protease, demonstrating in these two representative cases that convergence is accelerated by orders of magnitude.

First principles study of the optical contrast in phase change materials.

We study from first principles the optical properties of the phase change materials Ge(2)Sb(2)Te(5) (GST), GeTe and Sb(2)Te(3) in the crystalline phase and in realistic models of the amorphous phase generated by quenching from the melt in ab initio molecular dynamics simulations. The calculations reproduce the strong optical contrast between the crystalline and amorphous phases measured experimentally and exploited in optical data storage. It is demonstrated that the optical contrast is due to a change in the optical matrix elements across the phase change in all the compounds. It is concluded that the reduction of the optical matrix elements in the amorphous phases is due to angular disorder in p-bonding which dominates the amorphous network in agreement with previous proposals (Huang and Robertson 2010 Phys. Rev. B 81 081204) based on calculations on crystalline models.

Description of liver disease in a cohort of HIV/HBV coinfected patients.

BACKGROUND: Factors associated with advanced liver disease have been incompletely explored in HIV/HBV coinfected patients. OBJECTIVES: To describe liver-related morbidity, mortality, and related risk factors, in HIV/HBV coinfected patients. STUDY DESIGN: We followed-up 107 consecutive HIV/HBV coinfected patients. Clinical, biological and virological data were collected every 3 months. Liver-related mortality and a composite score were used to define advanced liver disease. RESULTS: The patients were mainly sub-Saharan Africans (61%) or Europeans (33%). Forty-four percent of patients had liver biopsy, 78% of patients received lamivudine. Advanced liver disease (ALD) was diagnosed in 19/107 patients during follow-up (mean 4.8 years): 10 extensive fibrosis, 5 cirrhosis, 3 hepatocellular carcinoma resulting from cirrhosis, and 1 fulminant hepatitis following lamivudine withdrawal. Eleven patients died, 4 from HBV-related liver disease. In univariate analysis, male gender, mean HIV and HBV viral loads, and raised AST/ALT transaminases were associated with increased risk of ALD. The strongest associations, in a multivariate model, were mean AST transaminase and cumulated time receiving lamivudine, with a favourable effect. 39% of patients with increased mean AST presented with ALD, versus 7% when normal mean AST (Relative Risk 5.5). CONCLUSIONS: During HIV/HBV coinfection, transaminase levels are strongly associated with ALD. Normal mean AST has a high negative predictive value, contrary to previously reported data in HIV/HCV patients.

Unravelling the mechanism of pressure induced amorphization of phase change materials.

Based on ab initio molecular dynamics simulations, we identify the atomistic mechanism of the pressure induced amorphization of Ge(2)Sb(2)Te(5). The simulations reveal that homopolar Ge/Sb bonds appear in cubic Ge(2)Sb(2)Te(5) under pressure, giving rise to square rings rotated by 45 degrees with respect to the crystalline axis whose formation is induced by the displacement of Te atoms filling the voids of neighboring Ge/Sb stoichiometric vacancies. The concentration of these topological defects increases with pressure up to 21 GPa at which the system is destabilized and transforms into an amorphous phase in agreement with experiments.

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.

Metadynamics is a widely used and successful method for reconstructing the free-energy surface of complex systems as a function of a small number of suitably chosen collective variables. This is achieved by biasing the dynamics of the system. The bias acting on the collective variables distorts the probability distribution of the other variables. Here we present a simple reweighting algorithm for recovering the unbiased probability distribution of any variable from a well-tempered metadynamics simulation. We show the efficiency of the reweighting procedure by reconstructing the distribution of the four backbone dihedral angles of alanine dipeptide from two and even one dimensional metadynamics simulation.

First-principles study of crystalline and amorphous Ge(2)Sb(2)Te(5) and the effects of stoichiometric defects.

Based on ab initio molecular dynamics simulations, we investigated the structural, electronic and vibrational properties of cubic and amorphous Ge(2)Sb(2)Te(5) (GST) phase change material, focusing in particular on the effects of defects in stoichiometry on the electronic properties. It turned out Ge/Sb deficiencies (excess) in the cubic phase induce a shift of the Fermi level inside the valence (conduction) bands. In contrast, the amorphous network is flexible enough to accommodate defects in stoichiometry, keeping the Fermi level pinned at the center of the bandgap (at zero temperature). Changes in the structural and electronic properties induced by the use of hybrid functionals (HSE03, PBE0) instead of gradient corrected functionals (PBE) are addressed as well. Analysis of vibrational spectra and Debye-Waller factors of cubic and amorphous GST is also presented.

Investigating the polymorphism in PR179: a combined crystal structure prediction and metadynamics study.

The polymorphism of an industrial important pigment (PR179) was studied with a combination of standard crystal structure prediction and metadynamics. The former provided a starting set of candidate polymorphs whose structural and thermal stability were then probed by metadynamics. Moreover, metadynamics allowed for exploring the free energy surface to look for other possible polymorphs that were not included in the original set. Our calculations indicate that two structures have a high structural stability and are therefore good candidates to be found in experiments. The lower energy phase of the two indeed corresponds to the known polymorph, and we suggest that the other might be a metastable polymorph not yet experimentally discovered.

HCl hydrates as model systems for protonated water.

Ab initio molecular dynamics simulations are presented of vibrational dynamics and spectra of crystal HCl hydrates. Depending on the composition, the hydrates include distinct protonated water forms, which in their equilibrium structures approximate either the Eigen ion H3O+(H2O)3 (in the hexahydrate) or the Zundel H2O...H+...OH2 ion (in the di- and trihydrate). Thus, the hydrates offer the opportunity to study spectra and dynamics of distinct species of protonated water trapped in a semirigid solvating environment. The experimentally measured spectra are reproduced quite well by BLYP/DZVP-level calculations employing Fourier transform of the system dipole. The large overall width (800-1000 cm-1) of structured proton bands reflects a broad range of solvating environments generated by crystal vibrations. The aqueous HCl solution was also examined in search of an objective criterion for separating the contributions of "Zundel-like" and "Eigen-like" protonated forms. It is suggested that no such criterion exists since distributions of proton-related structural properties appear continuous and unimodal. Dipole derivatives with respect to OH and O...H+ stretches in water and protonated water were also investigated to advance the understanding of the corresponding IR intensities. The effects of H bonding and solvation on the intensities were analyzed with the help of the Wannier centers' representation of electron density.

Elusive structure of HCl monohydrate.

The study addresses the structure of crystalline HCl monohydrate which is composed of H3O+ and Cl-. The published x-ray diffraction patterns indicate an element of disorder, the nature of which is debated in the literature and is addressed in the present study. The computational investigations include searches for alternative crystal structures employing an empirical potential, and on-the-fly simulations as implemented in the density functional code QUICKSTEP employing Gaussian basis sets. The experimental work focuses on Fourier-transform infrared (FTIR) spectra of crystal nanoparticles. Simulations of FTIR spectra and of the x-ray diffraction patterns are consistent with crystal monohydrate structure composed of ferroelectric domains, joined by "boundary tissue" of antiferroelectric structure.

A new glance at HCl-monohydrate spectroscopy, using on-the-fly dynamics.

On-the-fly dynamics is used to analyze the remarkably anharmonic infrared spectroscopy of crystalline HCl monohydrate, an ionic solid composed of H3O+ and Cl-. The dominant intense infrared feature is shown to originate from specific sections of the hydronium trajectory, in which one of the H-atoms interacts strongly with a neighboring Cl-.

Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail.

The ability of calcium-bound calmodulin (CaM) to recognize most of its target peptides is caused by its binding to two hydrophobic residues ('anchors'). In most of the CaM complexes, the anchors pack against the hydrophobic pockets of the CaM domains and are surrounded by fully conserved Met side chains. Here, by using metadynamics simulations, we investigate quantitatively the energetics of the final step of this process using the M13 peptide, which has a high affinity and spans the sequence of the skeletal myosin light chain kinase, an important natural CaM target. We established the accuracy of our calculations by a comparison between calculated and NMR-derived structural and dynamical properties. Our calculations provide novel insights into the mechanism of protein/peptide recognition: we show that the process is associated with a free energy gain similar to that experimentally measured for the CaM complex with the homologous smooth muscle MLCK peptide (Ehrhardt et al., 1995, Biochemistry 34, 2731). We suggest that binding is dominated by the entropic effect, in agreement with previous proposals. Furthermore, we explain the role of conserved methionines by showing that the large flexibility of these side chains is a key feature of the binding mechanism. Finally, we provide a rationale for the experimental observation that in all CaM complexes the C-terminal domain seems to be hierarchically more important in establishing the interaction.

Exploration of NVE classical trajectories as a tool for molecular crystal structure prediction, with tests on ice polymorphs.

Following an initial Communication [Buch et al., J. Chem. Phys. 123, 051108 (2005)], a new molecular-dynamics-based approach is explored to search for candidate crystal structures of molecular solids corresponding to minima of the enthalpy. The approach is based on the observation of phase transitions in an artificial periodic system with a small unit cell and relies on the existence of an optimal energy range for observing freezing to low-lying minima in the course of classical trajectories. Tests are carried out for O structures of nine H2O-ice polymorphs. NVE trajectories for a range of preimposed box shapes display freezing to the different crystal polymorphs whenever the box dimensions approximate roughly the appropriate unit cell; the exception is ice II for which freezing requires unit cell dimensions close to the correct ones. In an alternate version of the algorithm, an initial box shape is picked at random and subsequently readjusted at short trajectory intervals by enthalpy minimization. Tests reveal the existence of ice forms which are "difficult" and "easy" to locate in this way. The former include ice IV, which is also difficult to crystallize experimentally from the liquid, and ice II, which does not interface with the liquid in the phase diagram. On the other hand, the latter crystal search procedure located successfully the remaining seven ice polymorphs, including ice V, which corresponds to the most complicated structure of all ice phases, with a monoclinic cell of 28 molecules.

A new molecular-dynamics based approach for molecular crystal structure search.

A new molecular-dynamics based approach is proposed to search for candidate crystal structures of molecular solids. The procedure is based on the observation of spontaneous transitions between ordered and disordered states in molecular-dynamics simulations of an artificial periodic system with a small unit cell. In such a way only the most stable structures are automatically selected. The method can be applied to the solution of crystal structures from low-quality or very complex diffraction data. Tests are presented for H2O-ice polymorphs.